{
    "name":"run-command example pipeline",
    "components":{
        "bwa-mem": {
            "script": "run-command",
            "script_version": "master",
            "repository": "arvados",
            "script_parameters": {
                "command": [
                    "bwa",
                    "mem",
                    "-t",
                    "$(node.cores)",
                    "$(glob $(dir $(reference_collection))/*.fasta)",
                    "$(glob $(dir $(sample))/*_1.fastq)",
                    "$(glob $(dir $(sample))/*_2.fastq)"
                ],
                "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam",
                "reference_collection": {
                    "required": true,
                    "dataclass": "Collection"
                },
                "sample": {
                    "required": true,
                    "dataclass": "Collection"
                }
            }
        }
    }
}